ABSTRACT
BACKGROUND@#Microsatellite instability (MSI) is a key biomarker for cancer immunotherapy and prognosis. Integration of MSI testing into a next-generation-sequencing (NGS) panel could save tissue sample, reduce turn-around time and cost, and provide MSI status and comprehensive genomic profiling in single test. We aimed to develop an MSI calling model to detect MSI status along with the NGS panel-based profiling test using tumor-only samples.@*METHODS@#From January 2019 to December 2020, a total of 174 colorectal cancer (CRC) patients were enrolled, including 31 MSI-high (MSI-H) and 143 microsatellite stability (MSS) cases. Among them, 56 paired tumor and normal samples (10 MSI-H and 46 MSS) were used for modeling, and another 118 tumor-only samples were used for validation. MSI polymerase chain reaction (MSI-PCR) was performed as the gold standard. A baseline was built for the selected microsatellite loci using the NGS data of 56 normal blood samples. An MSI detection model was constructed by analyzing the NGS data of tissue samples. The performance of the model was compared with the results of MSI-PCR.@*RESULTS@#We first intersected the target genomic regions of the NGS panels used in this study to select common microsatellite loci. A total of 42 loci including 23 mononucleotide repeat sites and 19 longer repeat sites were candidates for modeling. As mononucleotide repeat sites are more sensitive and specific for detecting MSI status than sites with longer length motif and the mononucleotide repeat sites performed even better than the total sites, a model containing 23 mononucleotide repeat sites was constructed and named Colorectal Cancer Microsatellite Instability test (CRC-MSI). The model achieved 100% sensitivity and 100% specificity when compared with MSI-PCR in both training and validation sets. Furthermore, the CRC-MSI model was robust with the tumor content as low as 6%. In addition, 8 out of 10 MSI-H samples showed alternations in the four mismatch repair genes ( MLH1 , MSH2 , MSH6 , and PMS2 ).@*CONCLUSION@#MSI status can be accurately determined along the targeted NGS panels using only tumor samples. The performance of mononucleotide repeat sites surpasses loci with longer repeat motif in MSI calling.
Subject(s)
Humans , Microsatellite Instability , Colorectal Neoplasms/diagnosis , Microsatellite Repeats/genetics , DNA Mismatch RepairABSTRACT
Objective To investigate the association between primary sclerosing cholangitis (PSC) and colorectal cancer (CRC) by using two-sample Mendelian randomization (TSMR). Methods The single nucleotide polymorphism (SNP) data associated with PSC and CRC were obtained from Finland Biobank and UK Biobank, respectively. A secondary data analysis was performed for all pooled data based on genome-wide association studies to select the genetic loci closely associated with PSC as instrumental variables, and TSMR was conducted by seven methods, i.e., Egger regression in Mendelian randomization, weighted median, inverse variance weighted (IVW) random effects model, maximum likelihood, linear weighted median, IVW radial method, and IVW fixed effects model. Odds ratio (OR) value was used to evaluate the causal relationship between PSC and the risk of CRC. Results There was a positive causal relationship between gene predicted PSC and CRC, and with the IVW fixed effects model as an example, genetically determined patients with PSC could increase the risk of CRC ( OR =1.002 243, 95% confidence interval: 1.001 319-1.003 167). TSMR results showed no heterogeneity ( P =0.87) or horizontal pleiotropy ( P =0.95). The three instrumental variables selected for PSC were strong instrumental variables ( F =11.86). Conclusion TSMR shows the genetic evidence for the association between PSC and the risk of CRC. Regardless of the presence or absence of inflammatory bowel disease, active enteroscopy screening among patients with PSC may help with the early identification and timely intervention of CRC.